Bioinformatics

Section edited by Frank Eisenhaber and Sandor Pongor

The Bioinformatics section will be the publishing channel for scientific articles that report about theoretical, computational and data analysis approaches applied to biological, medical and other life science related problems, and the results and insights that have been achieved with them. Special emphasis is given to manuscripts that deal with biological mechanism interpretation to biomolecular sequence data and data from other experimental high-throughput techniques. This section also covers all fields of bioinformatics and computational biology that might not be handled by other subsections of Biology Direct. Hypotheses are welcome as long as they are based on rigorous scientific standards and as they fit existing data. Manuscripts describing new methods or software developments need to demonstrate that a major improvement has been achieved, and this has led to either improved accuracy by orders of magnitude, lowered resource consumption and/or some new biological insight.

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  1. Application note

    Altools: a user friendly NGS data analyser

    Genotyping by re-sequencing has become a standard approach to estimate single nucleotide polymorphism (SNP) diversity, haplotype structure and the biodiversity and has been defined as an efficient approach to ...

    Salvatore Camiolo, Gaurav Sablok and Andrea Porceddu

    Biology Direct 2016 11:8

    Published on: 17 February 2016

  2. Research

    PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues

    In the past, many methods have been developed for peptide tertiary structure prediction but they are limited to peptides having natural amino acids. This study describes a method PEPstrMOD, which is an updated...

    Sandeep Singh, Harinder Singh, Abhishek Tuknait, Kumardeep Chaudhary, Balvinder Singh, S. Kumaran and Gajendra P. S. Raghava

    Biology Direct 2015 10:73

    Published on: 21 December 2015

  3. Review

    RNA motif discovery: a computational overview

    Genomic studies have greatly expanded our knowledge of structural non-coding RNAs (ncRNAs). These RNAs fold into characteristic secondary structures and perform specific-structure dependent biological function...

    Avinash Achar and Pål Sætrom

    Biology Direct 2015 10:61

    Published on: 9 October 2015

  4. Research

    The human disease network in terms of dysfunctional regulatory mechanisms

    Elucidation of human disease similarities has emerged as an active research area, which is highly relevant to etiology, disease classification, and drug repositioning. In pioneer studies, disease similarity wa...

    Jing Yang, Su-Juan Wu, Wen-Tao Dai, Yi-Xue Li and Yuan-Yuan Li

    Biology Direct 2015 10:60

    Published on: 8 October 2015

  5. Review

    Microarray experiments and factors which affect their reliability

    Oligonucleotide microarrays belong to the basic tools of molecular biology and allow for simultaneous assessment of the expression level of thousands of genes. Analysis of microarray data is however very compl...

    Roman Jaksik, Marta Iwanaszko, Joanna Rzeszowska-Wolny and Marek Kimmel

    Biology Direct 2015 10:46

    Published on: 3 September 2015

  6. Review

    Experiences with workflows for automating data-intensive bioinformatics

    High-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring bioinformaticians to use high-performance computing resources and car...

    Ola Spjuth, Erik Bongcam-Rudloff, Guillermo Carrasco Hernández, Lukas Forer, Mario Giovacchini, Roman Valls Guimera, Aleksi Kallio, Eija Korpelainen, Maciej M Kańduła, Milko Krachunov, David P Kreil, Ognyan Kulev, Paweł P. Łabaj, Samuel Lampa, Luca Pireddu, Sebastian Schönherr…

    Biology Direct 2015 10:43

    Published on: 19 August 2015

  7. Research

    A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES)

    Antibiotic resistance is a major biomedical problem upon which public health systems demand solutions to construe the dynamics and epidemiological risk of resistant bacteria in anthropogenically-altered enviro...

    Marcelino Campos, Carlos Llorens, José M. Sempere, Ricardo Futami, Irene Rodriguez, Purificación Carrasco, Rafael Capilla, Amparo Latorre, Teresa M. Coque, Andres Moya and Fernando Baquero

    Biology Direct 2015 10:41

    Published on: 5 August 2015

  8. Research

    dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity

    Annotation transfer for function and structure within the sequence homology concept essentially requires protein sequence similarity for the secondary structural blocks forming the fold of a protein. A simplis...

    Wing-Cheong Wong, Choon-Kong Yap, Birgit Eisenhaber and Frank Eisenhaber

    Biology Direct 2015 10:39

    Published on: 1 August 2015

  9. Research

    De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods

    In the post-genomic era where sequences are being determined at a rapid rate, we are highly reliant on computational methods for their tentative biochemical characterization. The Pfam database currently contai...

    Richa Mudgal, Sankaran Sandhya, Nagasuma Chandra and Narayanaswamy Srinivasan

    Biology Direct 2015 10:38

    Published on: 31 July 2015

  10. Research

    Genome-scale identification and characterization of moonlighting proteins

    Moonlighting proteins perform two or more cellular functions, which are selected based on various contexts including the cell type they are expressed, their oligomerization status, and the binding of different...

    Ishita Khan, Yuqian Chen, Tiange Dong, Xioawei Hong, Rikiya Takeuchi, Hirotada Mori and Daisuke Kihara

    Biology Direct 2014 9:30

    Published on: 11 December 2014

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